scholarly journals The m6A RNA Modification Modulates Gene Expression and Fibrosis-Related Pathways in Hypertrophic Scar

2021 ◽  
Vol 9 ◽  
Author(s):  
Si-Yu Liu ◽  
Jun-Jie Wu ◽  
Zhong-hua Chen ◽  
Ming-Li Zou ◽  
Ying-ying Teng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Pcr ◽  
Hypertrophic Scar ◽  
Bioinformatics Analysis ◽  
Gene Expression Regulation ◽  
Normal Skin ◽  
Rna Modification ◽  
Real Time Quantitative Pcr ◽  
Mrna Transcripts ◽  
Differentially Expressed Mrna

Purpose: To systematically analyze the overall m6A modification pattern in hyperplastic scars (HS).Methods: The m6A modification patterns in HS and normal skin (NS) tissues were described by m6A sequencing and RNA sequencing, and subsequently bioinformatics analysis was performed. The m6A-related RNA was immunoprecipitated and verified by real-time quantitative PCR.Results: The appearance of 14,791 new m6A peaks in the HS sample was accompanied by the disappearance of 7,835 peaks. The unique m6A-related genes in HS were thus associated with fibrosis-related pathways. We identified the differentially expressed mRNA transcripts in HS samples with hyper-methylated or hypo-methylated m6A peaks.Conclusion: This study is the first to map the m6A transcriptome of human HS, which may help clarify the possible mechanism of m6A-mediated gene expression regulation.

m6A RNA modification modulates gene expression and cancer-related pathways in clear cell renal cell carcinoma

Epigenomics ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 87-99 ◽  
Author(s):  
Yimeng Chen ◽  
Cuixing Zhou ◽  
Yangyang Sun ◽  
Xiaozhou He ◽  
Dong Xue
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Gene Expression Regulation ◽  
Clear Cell ◽  
Rna Modification ◽  
Cell Renal Cell Carcinoma ◽  
Normal Tissues ◽  
Differentially Expressed Mrna

Aim: To systematically profile the global m6A modification pattern in clear cell renal cell carcinoma (ccRCC). Methods: m6A modification patterns in ccRCC and normal tissues were described via m6A sequencing and RNA sequencing, followed by bioinformatics analysis. m6A-related RNAs were immunoprecipitated and validated by quantitative real-time PCR (qPCR). Results: In total, 6919 new m6A peaks appeared with the disappearance of 5020 peaks in ccRCC samples. The unique m6A-related genes in ccRCC were associated with cancer-related pathways. We identified differentially expressed mRNA transcripts with hyper-methylated or hypo-methylated m6A peaks in ccRCC. Conclusion: This study presented the first m6A transcriptome-wide map of human ccRCC, which may shed lights on possible mechanisms of m6A-mediated gene expression regulation.

Human disease characterization: real-time quantitative PCR analysis of gene expression

2001 ◽  
Vol 6 (20) ◽  
pp. 1062-1067 ◽  
Author(s):  
James V Snider ◽  
Mark A Wechser ◽  
Izidore S Lossos
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Quantitative Pcr ◽  
Human Disease ◽  
Pcr Analysis ◽  
Real Time Quantitative Pcr

Validation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in strawberry fruits using different cultivars and osmotic stresses

Gene ◽  
2015 ◽  
Vol 554 (2) ◽  
pp. 205-214 ◽  
Author(s):  
Vanessa Galli ◽  
Joyce Moura Borowski ◽  
Ellen Cristina Perin ◽  
Rafael da Silva Messias ◽  
Julia Labonde ◽  
...  
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Quantitative Pcr ◽  
Reference Genes ◽  
Real Time Quantitative Pcr ◽  
Accurate Normalization

scholarly journals Establishing reference genes for use in real-time quantitative PCR analysis of early equine embryos

2011 ◽  
Vol 23 (2) ◽  
pp. 353 ◽  
Author(s):  
Damien B. B. P. Paris ◽  
Ewart W. Kuijk ◽  
Bernard A. J. Roelen ◽  
Tom A. E. Stout
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Quantitative Pcr ◽  
Embryo Development ◽  
Reference Genes ◽  
Stable Expression ◽  
Pcr Analysis ◽  
Blastocyst Development ◽  
Real Time Quantitative Pcr

Real-time quantitative PCR (qPCR) is invaluable for investigating changes in gene expression during early development, since it can be performed on the limited quantities of mRNA contained in individual embryos. However, the reliability of this method depends on the use of validated stably expressed reference genes for accurate data normalisation. The aim of the present study was to identify and validate a set of reference genes suitable for studying gene expression during equine embryo development. The stable expression of four carefully selected reference genes and one developmentally regulated gene was examined by qPCR in equine in vivo embryos from morula to expanded blastocyst stage. SRP14, RPL4 and PGK1 were identified by geNorm analysis as stably expressed reference genes suitable for data normalisation. RPL13A expression was less stable and changed significantly during the period of development examined, rendering it unsuitable as a reference gene. As anticipated, CDX2 expression increased significantly during embryo development, supporting its possible role in trophectoderm specification in the horse. In summary, it was demonstrated that evidence-based selection of potential reference genes can reduce the number needed to validate stable expression in an experimental system; this is particularly useful when dealing with tissues that yield small amounts of mRNA. SRP14, RPL4 and PGK1 are stable reference genes suitable for normalising expression for genes of interest during in vivo morula to expanded blastocyst development of horse embryos.

scholarly journals Evaluation of putative reference genes for quantitative real-time PCR normalization inLilium regaleduring development and under stress

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1837 ◽  
Author(s):  
Qiang Liu ◽  
Chi Wei ◽  
Ming-Fang Zhang ◽  
Gui-Xia Jia
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Real Time ◽  
Quantitative Pcr ◽  
Biotic Stress ◽  
Reference Genes ◽  
Developmental Stages ◽  
Real Time Quantitative Pcr ◽  
The Stability ◽  
Experimental Treatments

Normalization to reference genes is the most common method to avoid bias in real-time quantitative PCR (qPCR), which has been widely used for quantification of gene expression. Despite several studies on gene expression,Lilium, and particularlyL. regale, has not been fully investigated regarding the evaluation of reference genes suitable for normalization. In this study, nine putative reference genes, namely18S rRNA,ACT,BHLH,CLA,CYP,EF1,GAPDH,SANDandTIP41, were analyzed for accurate quantitative PCR normalization at different developmental stages and under different stress conditions, including biotic (Botrytis elliptica), drought, salinity, cold and heat stress. All these genes showed a wide variation in their Cq (quantification Cycle) values, and their stabilities were calculated by geNorm, NormFinder and BestKeeper. In a combination of the results from the three algorithms,BHLHwas superior to the other candidates when all the experimental treatments were analyzed together;CLAandEF1were also recommended by two of the three algorithms. As for specific conditions,EF1under various developmental stages,SANDunder biotic stress,CYP/GAPDHunder drought stress, andTIP41under salinity stress were generally considered suitable. All the algorithms agreed on the stability ofSANDandGAPDHunder cold stress, while onlyCYPwas selected under heat stress by all of them. Additionally, the selection of optimal reference genes under biotic stress was further verified by analyzing the expression level ofLrLOXin leaves inoculated withB. elliptica. Our study would be beneficial for future studies on gene expression and molecular breeding ofLilium.

Sign in / Sign up

Export Citation Format

Share Document